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Galaxyfill

A program for filling up the missing part of protein structure

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GalaxyFill: A program for filling up the missing part of protein structure

0. Remark

The GalaxyFill distribution version supports only Linux 64-bit OS and binary files compiled with serial option. Linux 32-bit OS or binary files compiled with MPI option are not supported.

1. Installation

  1. Download the GalaxyFill program

  2. Unzip and place the downloaded files

    • unzip GalaxyFill.zip
    • mv GalaxyFill $GALAXY_HOME
      (example: GALAXY_HOME=/applic/GalaxyFill)
  3. Check the downloaded files

    • There should exist:
    • bin: directory for executables
      There should be build_initial_model and GalaxyFill
    • data: directory for data files
    • examples: directory for example files
  4. Set environment variable

    • export GALAXY_HOME=$GALAXY_HOME
      (example: export GALAXY_HOME=/applic/GalaxyFill)

2. How to use GalaxyFill

  1. Prepare the input protein structure in PDB format

    • You have to provide a protein structure in the PDB file format for structure refinement. Gaps (or chain breaks) are highly prohibited in the middle of the initial protein structure.
  2. Run GalaxyFill

    • Usage: $GALAXY_HOME/bin/GalaxyFill [-h] [-p INPUT PDB File] [-s INPUT FASTA File]
    • Input arguments and options:
      • -p or --pdb : Input protein structure file in PDB format (mendatory)
      • -s or --seq : Input protein sequence file in FASTA format (mendatory)
      • -o or --out : Output protein structure file name (optional, default=${Input PDB prefix}_fill.pdb)
      • -t or --title : Running title for GalaxyFill (optional, default=${Input PDB prefix})
  3. Output of GalaxyFill

    • The final refined model will be ${Input PDB prefix}_fill.pdb or designated by "-o/--out" option

3. Release log

4. References

5. Contact